This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2fm4

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 10:39, 11 September 2015

NMR structure of the phosphoryl carrier domain of pyruvate phosphate dikinase

Structural highlights

2fm4 is a 1 chain structure with sequence from "bacteroides_symbiosus"_stevens_1956 "bacteroides symbiosus" stevens 1956. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	ppdK ("Bacteroides symbiosus" Stevens 1956)
Activity:	Pyruvate, phosphate dikinase, with EC number 2.7.9.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[PPDK_CLOSY] Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Pyruvate phosphate dikinase (PPDK) is a multidomain protein that catalyzes the interconversion of ATP, pyruvate, and phosphate with AMP, phosphoenolpyruvate (PEP), and pyrophosphate using its central domain to transport phosphoryl groups between two distant active sites. In this study, the mechanism by which the central domain moves between the two catalytic sites located on the N-terminal and C-terminal domains was probed by expressing this domain as an independent protein and measuring its structure, stability, and ability to catalyze the ATP/phosphate partial reaction in conjunction with the engineered N-terminal domain protein (residues 1-340 of the native PPDK). The encoding gene was engineered to express the central domain as residues 381-512 of the native PPDK. The central domain was purified and shown to be soluble, monomeric (13,438 Da), and stable (deltaG = 4.3 kcal/mol for unfolding in buffer at pH 7.0, 25 degrees C) and to possess native structure, as determined by multidimensional heteronuclear NMR analysis. The main chain structure of the central domain in solution aligns closely with that of the X-ray structure of native PPDK (the root-mean-square deviation is 2.2 A). Single turnover reactions of [14C]ATP and phosphate, carried out in the presence of equal concentrations of central domain and the N-terminal domain protein, did not produce the expected products, in contrast to efficient product formation observed for the N-terminal central domain construct (residues 1-553 of the native PPDK). These results are interpreted as evidence that the central domain, although solvent-compatible, must be tethered by the flexible linkers to the N-terminal domain for the productive domain-domain docking required for efficient catalysis.

Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase.,Lin Y, Lusin JD, Ye D, Dunaway-Mariano D, Ames JB Biochemistry. 2006 Feb 14;45(6):1702-11. PMID:16460017^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lin Y, Lusin JD, Ye D, Dunaway-Mariano D, Ames JB. Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase. Biochemistry. 2006 Feb 14;45(6):1702-11. PMID:16460017 doi:10.1021/bi051816l

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2fm4"

Categories: Bacteroides symbiosus stevens 1956 | Pyruvate, phosphate dikinase | Ames, J B | Phosphohistidine carrier domain | Transferase

@@ Line 2: / Line 2: @@
 <StructureSection load='2fm4' size='340' side='right' caption='[[2fm4]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2fm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FM4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteroides_symbiosus"_stevens_1956 "bacteroides symbiosus" stevens 1956]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FM4 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ppdK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1512 Clostridium symbiosum])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ppdK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1512 "Bacteroides symbiosus" Stevens 1956])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2fm4 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fm4 OCA], [http://pdbe.org/2fm4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2fm4 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2fm4" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Clostridium symbiosum]]
+[[Category: Bacteroides symbiosus stevens 1956]]
 [[Category: Pyruvate, phosphate dikinase]]
 [[Category: Ames, J B]]
 [[Category: Phosphohistidine carrier domain]]
 [[Category: Transferase]]

2fm4

From Proteopedia

Revision as of 10:39, 11 September 2015

NMR structure of the phosphoryl carrier domain of pyruvate phosphate dikinase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox